The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
Regulatory divergence in Drosophila revealed by mRNA-seq
Open accessAbstract
The regulation of gene expression is critical for organismal function and is an important source of phenotypic diversity between species. Understanding the genetic and molecular mechanisms responsible for regulatory divergence is therefore expected to provide insight into evolutionary change. Using deep sequencing, we quantified total and allele-specific mRNA expression levels genome-wide in two closely related Drosophila species (D. melanogaster and D. sechellia) and their F(1) hybrids. We show that 78% of expressed genes have divergent expression between species, and that cis- and trans-regulatory divergence affects 51% and 66% of expressed genes, respectively, with 35% of genes showing evidence of both. This is a relatively larger contribution of trans-regulatory divergence than was expected based on prior studies, and may result from the unique demographic history of D. sechellia. Genes with antagonistic cis- and trans-regulatory changes were more likely to be misexpressed in hybrids, consistent with the idea that such regulatory changes contribute to hybrid incompatibilities. In addition, cis-regulatory differences contributed more to divergent expression of genes that showed additive rather than nonadditive inheritance. A correlation between sequence similarity and the conservation of cis-regulatory activity was also observed that appears to be a general feature of regulatory evolution. Finally, we examined regulatory divergence that may have contributed to the evolution of a specific trait--divergent feeding behavior in D. sechellia. Overall, this study illustrates the power of mRNA sequencing for investigating regulatory evolution, provides novel insight into the evolution of gene expression in Drosophila, and reveals general trends that are likely to extend to other species.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“These methods discard allelic multireads that map to both parents and fail to account for reads that are simultaneously genomic and allelic multireads.”
From RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations (2014) · cites this paper as McManus et al. 2010
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Therefore, after aligning reads, we excluded differentiating sites with fewer than 20 overlapping reads and used binomial exact tests with a false discovery rate threshold of 0.05 to test each differentiating site for a statistically significant difference in relative allelic abundance [15,27].”
From Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome (2013) · cites this paper as [15]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“two alternative strategies for aligning reads have been shown to eliminate the systematic bias in measures of relative ASE favoring the reference allele”
From Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome (2013) · cites this paper as [15]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692
The Genome Sequence of Drosophila melanogaster
Adams, M. D., Celniker, S., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000) · Science · doi:10.1126/science.287.5461.2185 · Cited by 5,902
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (2007) · Nature · doi:10.1038/nature06341 · Cited by 2,010
The evolutionary significance of cis-regulatory mutations
Wray, G. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2063 · Cited by 1,521
Genetics of gene expression surveyed in maize, mouse and man
Schadt, E. E., Monks, S. A., Drake, T. A., Lusis, A. J., Che, N., Colinayo, V. V., Ruff, T. G., Milligan, S. B., Lamb, J. R., Cavet, G., et al. (2003) · Nature · doi:10.1038/nature01434 · Cited by 1,501
THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION
Hoekstra, H. E., & Coyne, J. A. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00105.x · Cited by 985
Evolution at Two Levels: On Genes and Form
Carroll, S. B. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030245 · Cited by 882
Cited by
Sorted by citations
Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence
Wittkopp, P. J., & Kalay, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3095 · Cited by 1,231
Self-citationComputational and analytical challenges in single-cell transcriptomics
Stegle, O., Teichmann, S. A., & Marioni, J. C. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3833 · Cited by 1,170
Trans effects on gene expression can drive omnigenic inheritance
Liu, X., Li, Y. I., & Pritchard, J. K. (2019) · Cell · doi:10.1016/j.cell.2019.04.014 · Cited by 523
From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
Marinov, G. K., Williams, B. A., McCue, K., Schroth, G. P., Gertz, J., Myers, R. M., & Wold, B. J. (2014) · Genome Research · doi:10.1101/gr.161034.113 · Cited by 468
The Genetics of Hybrid Incompatibilities
Maheshwari, S., & Barbash, D. A. (2011) · Annual Review of Genetics · doi:10.1146/annurev-genet-110410-132514 · Cited by 439
Metadata
- Authors
- McManus, C. J., Coolon, J. D., Duff, M. O., Eipper-Mains, J., Graveley, B. R., & Wittkopp, P. J.
- Affiliations
- University of Connecticut (US)
- University of Michigan (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-03-30
- Volume
- 20
- Issue
- 6
- Pages
- 816-825
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2877578
- OpenAlex
- W2121547736
- Cited by
- 381
- References
- 51
- Citations by year
- 2026: 16 · 2025: 16 · 2024: 19 · 2023: 18 · 2022: 33 · 2021: 26 · 2020: 34 · 2019: 18 · 2018: 17 · 2017: 16 · 2016: 26 · 2015: 31 · 2014: 27 · 2013: 24 · 2012: 31
- Type
- posted content
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Alfred P. Sloan Foundation
- March of Dimes Foundation (5-FY07-181)
- University of Michigan
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM062516)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- regulatory divergence, cis-regulatory divergence, gene expression evolution, Drosophila sechellia, Drosophila melanogaster, interspecific hybrids, hybrid incompatibility, allele-specific expression, additive inheritance, phenotypic diversity
- MeSH terms
- Animals, Drosophila, Gene Expression Regulation, RNA, Messenger, Species Specificity, Evolution, Molecular, Gene Expression Profiling
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
